From d4a0c82d002e76c0aac45f13a985aeeea0bea293 Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Mon, 1 Jul 2024 22:09:49 -0700
Subject: [PATCH] some ruff fixes

---
 nwb_linkml/src/nwb_linkml/__init__.py         |  9 ++++++-
 .../src/nwb_linkml/adapters/__init__.py       | 14 ++++++++++
 nwb_linkml/src/nwb_linkml/adapters/adapter.py | 26 +++++++++++--------
 nwb_linkml/{ => tests}/conftest.py            |  0
 pyproject.toml                                | 10 ++++---
 5 files changed, 43 insertions(+), 16 deletions(-)
 rename nwb_linkml/{ => tests}/conftest.py (100%)

diff --git a/nwb_linkml/src/nwb_linkml/__init__.py b/nwb_linkml/src/nwb_linkml/__init__.py
index 1b76aaf..ace1adc 100644
--- a/nwb_linkml/src/nwb_linkml/__init__.py
+++ b/nwb_linkml/src/nwb_linkml/__init__.py
@@ -1,5 +1,12 @@
+"""
+NWB in LinkML
+"""
 from nwb_linkml.monkeypatch import apply_patches
 
 apply_patches()
 
-from nwb_linkml.config import Config
+from nwb_linkml.config import Config  # noqa: E402
+
+__all__ = [
+    "Config"
+]
diff --git a/nwb_linkml/src/nwb_linkml/adapters/__init__.py b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
index 9c2a1ac..db1da1f 100644
--- a/nwb_linkml/src/nwb_linkml/adapters/__init__.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
@@ -1,6 +1,20 @@
+"""
+Adapter classes for translating from NWB schema language to LinkML
+"""
+
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.classes import ClassAdapter
 from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.group import GroupAdapter
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
+
+__all__ = [
+    "Adapter",
+    "BuildResult",
+    "ClassAdapter",
+    "DatasetAdapter",
+    "GroupAdapter",
+    "NamespacesAdapter",
+    "SchemaAdapter",
+]
diff --git a/nwb_linkml/src/nwb_linkml/adapters/adapter.py b/nwb_linkml/src/nwb_linkml/adapters/adapter.py
index fd68fba..b4b2641 100644
--- a/nwb_linkml/src/nwb_linkml/adapters/adapter.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/adapter.py
@@ -13,11 +13,13 @@ from typing import (
     Type,
     TypeVar,
     TypeVarTuple,
+    Union,
     Unpack,
 )
 
 from linkml_runtime.linkml_model import (
     ClassDefinition,
+    Definition,
     SchemaDefinition,
     SlotDefinition,
     TypeDefinition,
@@ -26,11 +28,15 @@ from pydantic import BaseModel
 
 from nwb_schema_language import Attribute, Dataset, Group, Schema
 
-# SchemaDefClass = dataclass(SchemaDefinition).__pydantic_model__
-
+T = TypeVar("T", Dataset, Attribute, Schema, Group, BaseModel)
+Ts = TypeVarTuple("Ts")
+Td = TypeVar('Td', bound=Union[Definition,SchemaDefinition,TypeDefinition])
 
 @dataclass
 class BuildResult:
+    """
+    Container class for propagating nested build results back up to caller
+    """
     # pass
     schemas: List[SchemaDefinition] = field(default_factory=list)
     classes: List[ClassDefinition] = field(default_factory=list)
@@ -38,12 +44,12 @@ class BuildResult:
     types: List[TypeDefinition] = field(default_factory=list)
 
     def __post_init__(self):
-        for field in ("schemas", "classes", "slots", "types"):
-            attr = getattr(self, field)
+        for a_field in ("schemas", "classes", "slots", "types"):
+            attr = getattr(self, a_field)
             if not isinstance(attr, list):
-                setattr(self, field, [attr])
+                setattr(self, a_field, [attr])
 
-    def _dedupe(self, ours, others):
+    def _dedupe(self, ours: List[Td], others: List[Td]) -> List[Td]:
         existing_names = [c.name for c in ours]
         others_dedupe = [o for o in others if o.name not in existing_names]
         return others_dedupe
@@ -80,11 +86,9 @@ class BuildResult:
         return out_str
 
 
-T = TypeVar("T", Dataset, Attribute, Schema, Group, BaseModel)
-Ts = TypeVarTuple("Ts")
-
-
 class Adapter(BaseModel):
+    """Abstract base class for adapters"""
+
     @abstractmethod
     def build(self) -> "BuildResult":
         """
@@ -101,7 +105,7 @@ class Adapter(BaseModel):
         yield input
         if isinstance(input, BaseModel):
 
-            for key in input.model_fields.keys():
+            for key in input.model_fields:
                 # Special case where SchemaAdapter Imports are themselves
                 # SchemaAdapters that should be located under the same
                 # NamespacesAdapter when it's important to query across SchemaAdapters,
diff --git a/nwb_linkml/conftest.py b/nwb_linkml/tests/conftest.py
similarity index 100%
rename from nwb_linkml/conftest.py
rename to nwb_linkml/tests/conftest.py
diff --git a/pyproject.toml b/pyproject.toml
index 287c4f2..0d7a7e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,9 +49,9 @@ select = [
     ## ----------
     # pydocstyle
     # undocumented public objects
-    "D100", "D101", "D102", "D103", "D104", "D106", "D107",
+    "D100", "D101", "D102", "D103", "D104", "D106",
     # indentation
-    "D207", "D208",
+    "D207", "D208", "D209",
     # whitespace
     "D210", "D211",
     # emptiness
@@ -65,12 +65,13 @@ ignore = [
     "UP006", "UP035",
     # | for Union types (only supported >=3.10
     "UP007", "UP038",
-    # docstrings for __init__
-    "D107",
 ]
 
 fixable = ["ALL"]
 
+[tool.ruff.lint.per-file-ignores]
+"**/tests/**.py" = ["D", "ANN"]
+
 [tool.mypy]
 plugins = [
     "pydantic.mypy"
@@ -86,5 +87,6 @@ warn_unreachable = true
 
 [tool.black]
 target-version = ['py38', 'py39', 'py310', 'py311']
+enable-unstable-feature = ["string_processing"]
 include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$"
 line-length = 100
\ No newline at end of file